[maker-devel] MAKER not calling RepeatMasker exe indicated in maker_exe.ctl

[Carson Holt]

The conda installation of RepeatMasker runs oddly. It does not appear to run the ./configure script during setup, and is missing files inside the repeat library as a result.

--Carson


> On Feb 4, 2019, at 2:00 AM, Lior Glick <liorglck at gmail.com> wrote:
> 
> Dear MAKER users,
> 
> I've been using MAKER for a while now, with RepeatMasker installed locally. By that I mean that I can type 'RepeatMasker' in my terminal and the software is initiated. Typing 'which RepeatMasker' shows the correct local path.
> I also use this path as value for the maker_exe.ctl parameter 'RepeatMasker'.
> Trying to generalize my working environment, I am trying to use a conda env <https://anaconda.org/bioconda/maker> which is capable of running MAKER. This env comes with RepeatMasker as well. Once I activate this env, I can still run RepeatMasker, but it points to a different path. When I run MAKER within this env, it fails right away with the error message:
> ERROR: Could not determine if RepBase is installed
> Running the same configuration files locally (i.e. outside the conda env) results in a successful run.
> This leads me to think that MAKER is not actually using the path indicated in the maker_exe.ctl file, and rather looks for RepeatMasker in $PATH or something similar. Is that the expected behavior? Any suggestions of how to overcome this issue?
> 
> Thanks and best regards,
> Lior
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